[gmx-users] Getting ligand's topology

Sun Aug 19 16:20:53 CEST 2018

Hi.

First, I feel grimaces users may not entertain other discussions in grimace
forum. You can directly mail me if it’s something apart from gromacs.

Then, I am not sure about other servers.

Looking at your str file, I would say that it definitely need some work on
our molecule. As I said before try zinc database.

Thank you

On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad <
mahdisobatinezhad at gmail.com> wrote:

> thanks.
> if I use MATCH server or swissparam, I can trust to their results?!
>
> And this is my error when I use CGenFF:
> "readmol2 warning: non-unique atoms were renamed. Now processing molecule
> mae ..."
>
> And this is my output of penalty:
>
> * Toppar stream file generated by * CHARMM General Force Field (CGenFF)
> program version 2.2.0 * For use with CGenFF version 4.0 * read rtf card
> append * Topologies generated by * CHARMM General Force Field (CGenFF)
> program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score of
> the associated parameters. ! Penalties lower than 10 indicate the analogy
> is fair; penalties between 10 ! and 50 mean some basic validation is
> recommended; penalties higher than ! 50 indicate poor analogy and mandate
> extensive validation/optimization. RESI mae 0.000 ! param penalty= 198.400
> ; charge penalty= 142.287 GROUP ! CHARGE CH_PENALTY ATOM C1 CG2R61 0.227 !
> 0.000 ATOM C2 CG2R61 -0.117 ! 2.688 ATOM C3 CG2R61 -0.003 ! 5.191 ATOM C4
> CG2R61 -0.117 ! 2.688 ATOM C5 CG2R61 0.227 ! 0.000 ATOM C6 CG2R61 0.217 !
> 0.000 ATOM H1 HGR61 0.115 ! 0.000 ATOM H2 HGR61 0.115 ! 0.000 ATOM O1 OG301
> -0.391 ! 0.000 ATOM O2 OG301 -0.391 ! 0.000 ATOM O3 OG301 -0.391 ! 0.000
> ATOM C7 CG331 -0.100 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGA3 0.090
> ! 0.000 ATOM H5 HGA3 0.090 ! 0.000 ATOM C8 CG331 -0.100 ! 0.000 ATOM H6
> HGA3 0.090 ! 0.000 ATOM H7 HGA3 0.090 ! 0.000 ATOM H8 HGA3 0.090 ! 0.000
> ATOM C9 CG331 -0.100 ! 0.000 ATOM H9 HGA3 0.090 ! 0.000 ATOM H10 HGA3 0.090
> ! 0.000 ATOM H11 HGA3 0.090 ! 0.000 ATOM C10 CG3C51 0.317 ! 142.287 ATOM N1
> NG3C51 -0.343 ! 101.066 ATOM C11 CG321 -0.072 ! 70.919 ATOM H12 HGA2 0.090
> ! 2.500 ATOM H13 HGA2 0.090 ! 2.500 ATOM C12 CG2R53 0.464 ! 90.248 ATOM N2
> NG2R50 -0.515 ! 21.469 ATOM N3 NG3C51 -0.417 ! 87.522 ATOM H14 HGP1 0.341 !
> 3.424 ATOM C13 CG321 0.028 ! 26.713 ATOM H15 HGA2 0.090 ! 2.659 ATOM N4
> NG3N1 -0.689 ! 58.305 ATOM C14 CG2R61 0.140 ! 19.097 ATOM C15 CG2R61 -0.110
> ! 13.488 ATOM C16 CG2R61 0.036 ! 13.718 ATOM C17 CG2R61 -0.112 ! 0.000 ATOM
> H16 HGR61 0.115 ! 0.000 ATOM C18 CG2R61 0.071 ! 0.000 ATOM C19 CG2R61
> -0.089 ! 0.000 ATOM H17 HGR61 0.115 ! 0.000 ATOM S SG311 -0.210 ! 105.411
> ATOM H18 HGP3 0.160 ! 4.359 ATOM H19 HGR62 0.144 ! 0.000 ATOM Cl1 CLGR1
> -0.152 ! 2.500 ATOM Cl2 CLGR1 -0.167 ! 0.000 ATOM HXT1 HGA1 0.090 ! 5.954
> ATOM HXT2 HGA2 0.090 ! 2.659 ATOM HN HGP1 0.394 ! 9.368 ATOM LP1 LPH 0.050
> ! on Cl1 ATOM LP2 LPH 0.050 ! on Cl2
>
>
> Thanks for your taking time
>
>
> On Sat, 18 Aug 2018 22:31 RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:
>
> > I cannot assist you much with the description of your ligand. But what I
> > have seen is, ring with N shows maximum penalities in most cases.
> >
> > When you optimise with mp2, the structure shows no much changes.
> > So penalty is same most time.
> >
> > Try to download file from Zinc15 database which is most preferred file
> >  cgenff. Still the penalty may exist in cse of N in ring. It could be
> > optimised using ffTK. Again I find your structure is pretty big which
> will
> > be time consuming. Or you have to adapt divide and conquer method, which
> is
> > going to be complicated. So it’s your wise choice always. Maybe others,
> > especially Dr. Justin or Dr. Mark could give you a better soln.
> >
> > Thank you
> >
> > On Sat, 18 Aug 2018 at 10:17 PM, Mahdi Sobati Nezhad <
> > mahdisobatinezhad at gmail.com> wrote:
> >
> > > Thanks for your help.
> > > my ligand is three rings that connects with a carbon and this rings
> have
> > > Nitrogen, oxygen, sulfur, carbon and Chlor...
> > > And high penaltys are just for that ring that contains Nitrogen, carbon
> > and
> > > sulfur
> > > And so on my choice is just using ffTK?!
> > >
> > >
> > > On Sat, 18 Aug 2018 21:05 RAHUL SURESH, <drrahulsuresh at gmail.com>
> wrote:
> > >
> > > > Hi.
> > > >
> > > > To resolve the penalties are bit complicated. Tools like ffTK can
> help
> > > you
> > > > do it. But output from ffTK is as in charmm and henceforth it take
> > > > additional work ( was difficult for me ) to modify it to Gromacs
> > > acceptable
> > > > format.
> > > >
> > > > I personally don’t appreciate this method as it is very time
> consuming
> > if
> > > > your structure is big and having penalties in dihedrals which again
> > make
> > > it
> > > > complicated.
> > > > Thank you
> > > >
> > > > On Sat, 18 Aug 2018 at 7:02 PM, Mahdi Sobati Nezhad <
> > > > mahdisobatinezhad at gmail.com> wrote:
> > > >
> > > > > Hi
> > > > > I'm a begginer in taking ligand's topology from CGENFF and my
> '.str'
> > > file
> > > > > have some high penalty numbers. What I can do?!
> > > > > And how I can do validation and optimization?!
> > > > > I read the FAQ in its server but I don't understand!!!
> > > > > Thanks
> > > > > --
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> > > > --
> > > > *Regards,*
> > > > *Rahul *
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> > *Rahul *
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-- 
*Regards,*
*Rahul *